Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility.
Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility.
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具有成对染色质可及性的可重复高通量单细胞全基因组测序。
DOI：
10.1016/j.crmeth.2023.100625
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发表时间：
2023-11-20
期刊：
影响因子：
--
通讯作者：
Adey AC
中科院分区：
文献类型：
--
作者：
Queitsch K;Moore TW;O'Connell BL;Nichols RV;Muschler JL;Keith D;Lopez C;Sears RC;Mills GB;Yardımcı GG;Adey AC
单细胞全基因组测序(ScWGS)能够评估单个细胞之间基因组水平的分子差异，这与实体瘤等遗传多样性系统特别相关。由于缺乏能够生产高通量剖面的无障碍平台，scWGS的应用受到限制。我们提出了一种技术，该技术利用核小体破坏方法与广泛采用的10倍基因组ATAC-SEQ工作流相结合，在没有新设备或定制试剂的情况下产生用于高通量拷贝数分析的scWGS图谱。我们进一步展示了使用来自ScaleBio的可商业获得的索引转座酶复合体进行样品多路传输，从而降低了每个样品的制备成本。最后，我们证明了带有介入的核小体破坏步骤的顺序索引标记允许从同一细胞生成ATAC和WGS数据，产生与单峰分析类似的数据。通过独家使用可获得的商业试剂，我们预计这些scWGS和scWGS+ATAC方法可以被研究界广泛采用。单细胞WGS与广泛使用的单细胞ATAC-SEQ工作流索引标记的集成使得scWGS实验的样本多路复用使用索引转座体的双重标记产生成对的ATAC和WGS图谱单细胞全基因组测序(ScWGS)是研究复杂、异质生物学的有力工具。这项研究的动机是建立一种仅依赖于商业上可获得的试剂和仪器的SCWGS方法，以使尽可能广泛的研究界能够获得这项技术。Queitsch等人。报道了一种在广泛使用的10倍基因组铬平台上使用试剂盒进行配对、单细胞全基因组测序和ATAC-SEQ的方法。该方法包括一种有效和可访问的策略，用于检查基因组变化和肿瘤亚克隆结构，使肿瘤进化研究能够为治疗开发提供信息。
Single-cell whole-genome sequencing (scWGS) enables the assessment of genome-level molecular differences between individual cells with particular relevance to genetically diverse systems like solid tumors. The application of scWGS was limited due to a dearth of accessible platforms capable of producing high-throughput profiles. We present a technique that leverages nucleosome disruption methodologies with the widely adopted 10× Genomics ATAC-seq workflow to produce scWGS profiles for high-throughput copy-number analysis without new equipment or custom reagents. We further demonstrate the use of commercially available indexed transposase complexes from ScaleBio for sample multiplexing, reducing the per-sample preparation costs. Finally, we demonstrate that sequential indexed tagmentation with an intervening nucleosome disruption step allows for the generation of both ATAC and WGS data from the same cell, producing comparable data to the unimodal assays. By exclusively utilizing accessible commercial reagents, we anticipate that these scWGS and scWGS+ATAC methods can be broadly adopted by the research community. Integration of single-cell WGS with widely available single-cell ATAC-seq workflows Indexed tagmentation enables sample multiplexing for scWGS experiments Double tagmentation using indexed transposomes produces paired ATAC and WGS profiles Single-cell whole-genome sequencing (scWGS) is a powerful tool for studying complex, heterogeneous biology. The motivation for this study was to establish an scWGS method that relies only on commercially available reagents and instrumentation to make the technology accessible to the widest possible segment of the research community. Queitsch et al. report a method for paired, single-cell whole-genome sequencing and ATAC-seq using kits on the widely used 10× Genomics Chromium platform. The method comprises an effective and accessible strategy for examining genomic alterations and tumor subclonal structures, enabling tumor evolution studies that can inform therapeutic development.
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影响因子：
48
作者：
Vitak SA;Torkenczy KA;Rosenkrantz JL;Fields AJ;Christiansen L;Wong MH;Carbone L;Steemers FJ;Adey A
通讯作者：
Adey A
影响因子：
64.8
作者：
Navin N;Kendall J;Troge J;Andrews P;Rodgers L;McIndoo J;Cook K;Stepansky A;Levy D;Esposito D;Muthuswamy L;Krasnitz A;McCombie WR;Hicks J;Wigler M
通讯作者：
Wigler M
影响因子：
3.7
作者：
Derrien T;Estellé J;Marco Sola S;Knowles DG;Raineri E;Guigó R;Ribeca P
通讯作者：
Ribeca P
影响因子：
64.8
作者：
Wang, Yong;Waters, Jill;Leung, Marco L.;Unruh, Anna;Roh, Whijae;Shi, Xiuqing;Chen, Ken;Scheet, Paul;Vattathil, Selina;Liang, Han;Multani, Asha;Zhang, Hong;Zhao, Rui;Michor, Franziska;Meric-Bernstam, Funda;Navin, Nicholas E.
通讯作者：
Navin, Nicholas E.
影响因子：
64.5
作者：
Kim C;Gao R;Sei E;Brandt R;Hartman J;Hatschek T;Crosetto N;Foukakis T;Navin NE
通讯作者：
Navin NE